Genethics and genomics in the community
Andrew Papanikitas, John Spicer in Handbook of Primary Care Ethics, 2017
The 20,000 genes we carry in each cell are collectively the genome, comprising the exome (which does the protein coding) and the rest. Today, we can sequence the whole genome [whole genome sequencing (WGS)] including RNA or, being less costly, the exome [whole exome sequencing (WES)]. The methodologies and techniques behind sequencing technology can be used to identify high-risk genes such as BRCA1, associated with breast cancer, or rare gene variants such as those for developmental disorders. The findings from WGS or WES may affect reproductive choices or indeed treatment choices for various diseases in the future. It is likely that in years to come, the impact of these aspects of genomics will find a way into primary health care as our patients who undergo such tests seek help and advice, so that some understanding of what is now a large literature on genethics should be useful to a primary care clinician. Sequencing speed and accuracy is increasing and this makes determining the likelihood of pathogenicity much easier. Some costs are falling, making direct-to-consumer testing a reality, and others are extremely high, meaning that the techniques are available in the experimental and private healthcare settings only. Nonetheless, clinical utility may be difficult to determine. Variants of uncertain significance inevitably arise, the genomic equivalent of the clinically unclassifiable abnormality in a complex patient, which exemplifies a disjunction between individual genotype (the genetic code) and phenotype (the physical expression of the code).4
Will Systems Biology Transform Clinical Decision Support?
Paul Cerrato, John Halamka in Reinventing Clinical Decision Support, 2020
Studying network medicine’s essential components is also providing useful insights into the nature of asthma, as we discussed earlier. Oligonucleotide microarrays and sequencing are homing in on single-nucleotide polymorphisms (SNPs) that may be involved in the pathophysiology of asthma, for instance. Some of the strongest evidence comes from genome-wide association studies (GWAS) that focus on the 17q21 locus, referring to chromosome 17—the lower q section, position 21. Four genes in this section of the chromosome—ORMDL3, GSDMB, ZPBP2, and IKZF3—have been linked to inflammatory response, a major problem for patients with asthma. GWAS also suggest that specific gene variants in the FLG gene contribute to atopic dermatitis in Europeans and Asians. The mutations are not usually found in Africans, as demonstrated by whole exome sequencing. (The exome is that fraction of the genome that contains protein-encoding DNA.)18
Advances in Non-Invasive Diagnosis of Single-Gene Disorders and Fetal Exome Sequencing
Carlos Simón, Carmen Rubio in Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
Genome and exome sequencing are technologies that examine the genome at a nucleotide level. NGS is achieved by sequencing many distributed, overlapping sites throughout the genome in a massively parallel manner.56,57 Briefly, for NGS library preparation, genomic DNA is sheared into 50–400 nt fragments, ligated to adapters, and purified. For panel or exome sequencing, an enrichment step is included to capture regions of interest using “DNA baits.” Massively parallel sequencing of the NGS library then rapidly and accurately derives the nucleotide sequences of each fragment, which are then aligned to a reference genome to detect potential sequence variants56–58 (Figure 27.3). Two quality parameters for NGS accuracy are the sequencing depth, which refers to the number of overlapping reads for each base-pair, and the breadth of sequence coverage, which is the fraction of the reference sequence that is covered at sufficient depth. The American College of Medical Genetics and Genomics (ACMG) recommends an average depth of ≥ 100-fold with 90–95% of the sequence covered at least 10-fold for diagnostic exome sequencing (ES).59 With recent advances in NGS technology, clinical laboratories can offer increasingly better sequencing depth and shorter turnaround time (TAT) to results, which is crucial for fetal ES.60,61
Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside
Published in Expert Review of Proteomics, 2021
Lauren C Beck, Claire L Granger, Andrea C Masi, Christopher J Stewart
Genetic predisposition to pediatric disease makes genomic studies of significant importance. Genomics is the study of the whole genome of an organism, and in a clinical context it can be used to map and identify genetic variants and potential risk factors that can contribute to certain diseases [34]. There are a number of genomic associated studies, namely genome-wide association studies (GWAS), whole genome sequencing (WGS) and whole exome sequencing (WES). GWAS looks to identify genetic variation associated with specific diseases by genotyping thousands of individuals for genetic markers, which then allows specific genetic variants to be associated with disease [35]. WGS aims to sequence the entire genome rather than just focusing on genetic markers, which ultimately captures the more rare genetic variants associated with both common and rare diseases [35,36]. Finally, WES involves sequencing the protein-coding regions of the genome, otherwise known as the exome. This approach is less expensive than WGS and well justified, since the vast majority of allelic variants known to underlie Mendelian disorders disrupt protein-coding sequences [37].
Whole exome sequencing in a large pedigree with DCM identifies a novel mutation in RBM20
Published in Acta Cardiologica, 2020
Tomas Robyns, Rik Willems, Johan Van Cleemput, Shalini Jhangiani, Donna Muzny, Richard Gibbs, James R. Lupski, Jeroen Breckpot, Koenraad Devriendt, Anniek Corveleyn
Comprehensive gene panel testing is the current cornerstone of clinical DNA testing for cardiogenetic diseases. Especially in DCM, which is genetically very heterogeneous, this approach makes clinical DNA testing feasible [2]. However, a definite mutation can only be identified in about 40% of the cases [2]. Whole exome sequencing is a powerful alternative, since it covers the whole protein coding sequence of the genome. Therefore, it might unravel a mutation, which is located in a region, that is not yet known to be associated with a specific disease and thus not included in a dedicated disease panel. Since WES results in an enormous amount of genetic variants, identifying the disease-causing mutation remains similar to looking for a needle in a haystack. Therefore, we applied WES on 2 distant affected family members, thereby reducing the number of variants of interest to only 3.8% of the initial number. After some additional filtering steps a limited number of variants remained, and co-segregation analysis by Sanger sequencing of these variants became feasible. The RBM20 variant was the only that fully co segregated with the affected family members. At the time the proband of the current pedigree underwent genetic testing, RBM20 was not yet established as a definite DCM causing gene and was not included on the gene panel that was performed earlier.
Next-generation sequencing and its application in diagnosis of retinitis pigmentosa
Published in Ophthalmic Genetics, 2019
Arash Salmaninejad, Jamshid Motaee, Mahsa Farjami, Maliheh Alimardani, Alireza Esmaeilie, Alireza Pasdar
Protein-coding genes constitute merely around 1% of the human genome although harbor 85% of the mutations with some effects on disease-related characters (53). Hence, impressive approaches for discriminating sequencing completely coding regions (i.e., ‘‘whole exome’’) have the potential to contribute to the conception of rare, common and heterogeneous human diseases. WES is widely used as targeted sequencing method. As the name propose, it is based on a system of amplification or capturing used to enrich or isolate only exons. This is done by primers or oligonucleotide probes (baits) for the regions of interest. WES analysis usually captures 35–100 Mb from DNA target areas depending on the reference annotation system in probe design and 3′ or 5′ untranslated regions (UTRs) in the investigational design. For example, NimbleGen covers about 96 Mb (64 Mb coding (C), 32 Mb UTR) (28). The exome constitutes less than 2% of the human genome however cover 85% of all mutations that effect human disease. Therefore, WES is a more cost-effective method than WGS in clinical application. In addition, it can effectively lead to a reliable diagnosis in about 20–30% of the cases where the patient had been previously left undiagnosed (54).